deep_research/.agents/workflows/deep-research-native.md

description

description
Run native biomedical Deep Research in Antigravity using roles, rules, skills, workflows, source receipts, and explicit approval gates.

Deep Research Native Workflow

Invoke as /deep-research-native <topic or slug>.

Step 0: Load Operating Context

• Load AGENTS.md.
• Load GEMINI.md.
• Load .agents/agents.md.
• Load .agents/rules/deep-research-antigravity.md.
• Load .agents/skills/antigravity-surface-adapter/SKILL.md.
• Load .agents/skills/method-selection/SKILL.md.
• Load relevant quality skills: search-strategy, source-quality, evidence-table, research-quality-gates, citation-manager, length-budget, output-hygiene.

Gate: if the active model has not loaded the above files, stop and ask the user to restart or explicitly mention them.

Step 1: Define The Research Problem

Act as Research Manager with Gemini 3 Flash.

Confirm:

• topic and slug
• report purpose
• target reader
• decision the report supports
• report type and expected length
• available input materials
• allowed search tools
• whether Python model-worker commands are forbidden or allowed

Create or confirm projects/<slug>/ and phase folders. Create or update projects/<slug>/continuation_state.json. Use Python only for scaffolding if helpful.

Gate: do not continue if purpose, audience, and decision use are unclear.

Step 2: Select Method

Ask the user to switch to Claude Opus 4.6 (Thinking).

Act as Phase 0-1 Strategist. Use method-selection.

Write a method decision note covering:

• selected method or method mix
• why it fits the scenario
• rejected methods and why
• evidence types required
• search routes by chapter or task axis
• expected artifacts

Save it as phase1/method_decision.md or embed the same content in phase1/research_brief.md with a clear heading.

Gate: do not default to McKinsey, MECE, or SCQA. Use them only when they fit the decision problem.

Step 3: Phase 0-1 Framing

Still using Claude Opus 4.6 (Thinking), produce:

• phase1/material_brief.md
• phase1/search_log.md
• phase1/method_decision.md
• phase1/assumptions.md
• phase1/framework.md
• phase1/research_brief.md
• phase1/research_brief.json
• phase1/unsupported_claims.md

Rules:

• Hypotheses without evidence must be labeled as hypotheses.
• Every searched claim must have a search receipt.
• Each chapter must state method, core question, likely evidence, and falsification route.

Gate: pause for user approval before Phase 2.

Step 4: Phase 2 Evidence And Drafting

Ask the user to switch to Gemini 3.1 Pro (Low).

Act as Evidence Analyst.

Produce:

• phase2/task_cards.json
• phase2/search_log.jsonl
• phase2/sources.jsonl
• phase2/rejected_sources.jsonl
• phase2/claims_ledger.jsonl
• phase2/coverage_matrix.md
• phase2/packets/*.json
• phase2/chapter_briefs/*.json
• phase2/compressed_findings/*.json
• phase2/drafts/chXX.md
• phase2/unsupported_claims.md

Rules:

• No tool receipt, no search claim.
• No source ID, no factual claim.
• Search snippets and AI summaries are leads only.
• Every packet must include search_receipts, sources, evidence_spans, counter_evidence, and unsupported_claims.
• Every core claim must be represented in claims_ledger.jsonl.
• Every chapter must pass a counter-search or falsification pass.
• Evidence gaps trigger delta retrieval before drafting or visible caveats if still unresolved.
• Draft chapters only from approved chapter briefs and compressed findings.

Gate: run research-quality-gates. Do not move to Phase 3 if packet evidence is missing, claim-ledger records are incomplete, unsupported claims are hidden, source independence is not tracked, or counter-evidence is absent.

Step 5: Phase 3 Review

Ask the user to switch to Gemini 3.1 Pro (High).

Act as Chief Reviewer.

Produce phase3/critique.md with:

• go / rework / fail decision
• structural critique
• method fit critique
• evidence gap list
• counter-evidence critique
• claim-ledger audit
• coverage matrix audit
• source-audit table for at least 10 core facts
• rework task list if needed

If the critique finds a critical evidence gap, create delta-retrieve tasks instead of asking Phase 4 to paper over the gap.

Gate: pause for user decision after critique.

Step 6: Phase 4 Finalization

Ask the user to switch to Claude Opus 4.6 (Thinking).

Act as Final Editor.

Produce:

• phase4/final_zh.md
• phase4/editorial_notes.md
• phase4/final_fact_check.md

Rules:

• Do not introduce new facts unless new sources and search logs are added first.
• Final facts must be a subset of verified or explicitly caveated claims_ledger.jsonl rows.
• Downgrade or mark claims that remain unsupported.
• Use deterministic rendering tools afterward for PDF/DOCX.

Gate: final output must pass citation and unsupported-claim review before rendering.